GENOME ANALYSIS RESPORT

Data used in this analysis

In this experiment the start set data are:

GENERAL DESCRIPTION

This resport show all the genome analysis information that included:

The taxonomy identification of problem strains as Shewanella.sp was based on Silva Taxonomy results (https://www.arb-silva.de/documentation/silva-taxonomy/). The species was identified by blastn of 16S RNA gene and the problematic strain genomes comparison with 120 complete genomes described on NCBI database. The complete genome of Shewanella.sp Pdp11 and partial genome of pathogenic and saprofit strains of shewanella were annotated using Dfast tool, by Clusters of Orthologous Groups (COG) and the number of genes asociated to categories were determinated. The transposons has been detected by ISEScan tool (https://github.com/xiezhq/ISEScan) which was complemented with tp_finder workflow for transposase and disrupt protein identification. The genomic islands were identify using IslandViewer 4 software, by API option. The genome comparison of Shewanella.sp Pdp11 and pathogenic strains allow us to identified the specific genes of pathogenic strains and their absent in probiotic.

16S RNA

The Table indicated the 16S RNA analysis of problem genomes was carry out by blatn. The top 10 for each strain with high identity and coverage value.

Ref strain identity coverage
Pdp11_1492R NR_178284.1_Shewanella_arctica 99.580 100
Pdp11_1492R NR_113967.1_Shewanella_hafniensis 99.055 100
Pdp11_1492R NR_041296.1_Shewanella_hafniensis 99.160 100
Pdp11_1492R NR_108852.1_Shewanella_seohaensis 99.160 100
Pdp11_1492R NR_044863.1_Shewanella_putrefaciens 98.950 100
Pdp11_1492R NR_119141.1_Shewanella_putrefaciens 98.845 100
Pdp11_1492R NR_025267.1_Shewanella_baltica 98.847 100
SdM1_1492R NR_108852.1_Shewanella_seohaensis 99.483 100
SdM1_1492R NR_178284.1_Shewanella_arctica 99.353 100
SdM1_1492R NR_044863.1_Shewanella_putrefaciens 99.224 100
SdM1_1492R NR_119141.1_Shewanella_putrefaciens 98.965 100
SdM1_1492R NR_113967.1_Shewanella_hafniensis 98.706 100
SdM1_1492R NR_041296.1_Shewanella_hafniensis 98.836 100
SdM1_1492R NR_116732.1_Shewanella_xiamenensis 98.708 100
SdM2_1492R NR_113582.1_Shewanella_putrefaciens 99.107 100
SdM2_1492R NR_119141.1_Shewanella_putrefaciens 99.106 99
SdM2_1492R NR_044863.1_Shewanella_putrefaciens 99.018 100
SdM2_1492R NR_104770.1_Shewanella_profunda 98.839 100
SH12_1492R NR_116732.1_Shewanella_xiamenensis 99.326 100
SH12_1492R NR_074798.1_Shewanella_oneidensis 99.038 100
SH12_1492R NR_036917.1_Shewanella_oneidensis 98.845 100
SH12_1492R NR_044863.1_Shewanella_putrefaciens 98.847 100
SH16_1492R NR_044863.1_Shewanella_putrefaciens 99.174 100
SH16_1492R NR_178284.1_Shewanella_arctica 99.174 100
SH16_1492R NR_119141.1_Shewanella_putrefaciens 99.071 100
SH16_1492R NR_113582.1_Shewanella_putrefaciens 98.762 100
SH16_1492R NR_116732.1_Shewanella_xiamenensis 98.763 100
SH4_1492R NR_116732.1_Shewanella_xiamenensis 99.217 100
SH4_1492R NR_074798.1_Shewanella_oneidensis 98.957 100
SH4_1492R NR_036917.1_Shewanella_oneidensis 98.783 100
SH6_1492R.fasta NR_044863.1_Shewanella_putrefaciens 99.285 100
SH6_1492R.fasta NR_119141.1_Shewanella_putrefaciens 99.081 100
SH6_1492R.fasta NR_178284.1_Shewanella_arctica 99.081 100
SH6_1492R.fasta NR_113582.1_Shewanella_putrefaciens 98.774 100
SH6_1492R.fasta NR_116732.1_Shewanella_xiamenensis 98.878 100
SH9_1492R NR_044863.1_Shewanella_putrefaciens 99.106 100
SH9_1492R NR_119141.1_Shewanella_putrefaciens 98.833 99

Identity of complete genome comparison

The heatmap represent the variability of identity in Shewanella genus based on 120 complete genomes of NCBI. The probiotic Shewanella.sp Pdp11 had high similarity to Shewanella baltica complete genomes.

Coverage of complete genome comparison

The heatmap represent the variability of coverage in Shewanella genus based on 120 complete genomes of NCBI.

Sybelia results

COG annotation

The Figure represent the annotation by Dfast of the 8 research strains of Shewanella.sp. The COG categories evidence the high number of genes on Pdp11 genome asociated to transposase, defense mechanisms and replication and repair.

Transposon identification

The Table evidence the transposons identified in Shewanella.sp Pdp11 genome and the disrupted proteina by transposase.

genome coordinate start tpfinder end tpfinder transposase protein disrupt protein
Q_Shewanella_Pdp11:850951:856278 2033 3326 A0A883CDA5 A0A4Y5YC98
Q_Shewanella_Pdp11:1261471:1266798 1992 3309 A0A883CDA5 A0A165J291
Q_Shewanella_Pdp11:1906106:1911827 2000 3723 A0A2K9AH24 A0A3Q9E364
Q_Shewanella_Pdp11:2693976:2700579 1969 4609 A0A2K8ZWT8 A0A2G1ZI34
Q_Shewanella_Pdp11:2990403:2995648 1999 3241 A0A2K8ZWA4 A3D7T2
Q_Shewanella_Pdp11:3053373:3058616 2049 3244 A0A2K8ZZ67 A0AA42UJ63
Q_Shewanella_Pdp11:3073685:3079406 1999 3725 A0A2K9AH24 A0A2R3EZ14
Q_Shewanella_Pdp11:4349020:4355949 1959 3354 A0A2K8ZPD2 A0A6G9QQZ7

Genomic Island

The Mobilome analysis included the genomic island identification, Shewanella. sp Pdp11 and SdM1 present 13 Genomic Island, a high value respect to other Shewanella strains

Genomic Island in Shewanella.sp Pdp11

The Shewanella. sp Pdp11 is a probiotic strain isolated in our research group and we identified a total of 13 Genomic Island in its genome sequence asociated to diverse function

Island_start Island_end Length Gene_ID Locus Product
128432 144890 16458 rsd LOCUS_01210 sigma D regulator
128432 144890 16458 secA LOCUS_01230 protein translocase subunit SecA
128432 144890 16458 LOCUS_01240 peptidase M23
128432 144890 16458 LOCUS_01250 DUF721 domain-containing protein
128432 144890 16458 lpxC LOCUS_01260 UDP-3-O-acyl-N-acetylglucosamine deacetylase
128432 144890 16458 ftsZ LOCUS_01270 cell division protein FtsZ
128432 144890 16458 ftsA LOCUS_01280 cell division protein FtsA
128432 144890 16458 ftsQ LOCUS_01290 cell division protein FtsQ
1350555 1360798 10243 groL LOCUS_11350 60 kDa chaperonin
1350555 1360798 10243 LOCUS_11360 group II intron reverse transcriptase/maturase
1350555 1360798 10243 hipB LOCUS_11390 antitoxin HipB
1350555 1360798 10243 LOCUS_11440 DUF2999 domain-containing protein
1457524 1477294 19770 LOCUS_12520 phage portal protein
1457524 1477294 19770 LOCUS_12530 ATP-dependent Clp protease proteolytic subunit
1457524 1477294 19770 LOCUS_12600 transcriptional regulator
1457524 1477294 19770 LOCUS_12700 integrase
1522675 1539963 17288 blaA LOCUS_13090 beta-lactamase
1522675 1539963 17288 LOCUS_13100 LysR family transcriptional regulator
1522675 1539963 17288 accADCB LOCUS_13110 carbamoyl phosphate synthase large subunit
1522675 1539963 17288 LOCUS_13150 diguanylate cyclase
1522675 1539963 17288 fusB LOCUS_13160 elongation factor G 2
1987801 2001908 14107 LOCUS_16900 phosphatidylinositol kinase
1987801 2001908 14107 LOCUS_16910 riboflavin-specific deaminase
1987801 2001908 14107 LOCUS_16920 iso-IS10R ORF
1987801 2001908 14107 rpoD LOCUS_17030 RNA polymerase sigma factor RpoD
2501325 2527562 26237 yncI LOCUS_21360 putative transposase YncI
2501325 2527562 26237 LOCUS_21370 TonB-dependent receptor
2501325 2527562 26237 LOCUS_21380 DUF3450 domain-containing protein
2501325 2527562 26237 ttpC LOCUS_21390 flagellar motor protein MotA
2501325 2527562 26237 exbB LOCUS_21400 TonB2 energy transduction system inner membrane component ExbB
2501325 2527562 26237 exbD LOCUS_21410 biopolymer transporter ExbD
2501325 2527562 26237 tonB2 LOCUS_21420 protein TonB
2501325 2527562 26237 LOCUS_21440 diguanylate cyclase
2501325 2527562 26237 ppiC LOCUS_21470 peptidyl-prolyl cis-trans isomerase
2501325 2527562 26237 rimJ LOCUS_21480 N-acetyltransferase GCN5
2501325 2527562 26237 LOCUS_21490 S4 RNA-binding domain protein
2501325 2527562 26237 LOCUS_21510 LysR family transcriptional regulator
2501325 2527562 26237 yfcA LOCUS_21520 UPF0721 transmembrane protein
2501325 2527562 26237 sbcD LOCUS_21530 nuclease SbcCD subunit D
2501325 2527562 26237 sbcC LOCUS_21540 nuclease SbcCD subunit C
2501325 2527562 26237 LOCUS_21550 subfamily M23B unassigned peptidase
2501325 2527562 26237 LOCUS_21590 RNA helicase
2674842 2703653 28811 thiK LOCUS_22900 aminoglycoside phosphotransferase
2674842 2703653 28811 LOCUS_22920 DoxD-like inner membrane protein
2674842 2703653 28811 ydjA LOCUS_22930 nitroreductase
2674842 2703653 28811 LOCUS_22940 N-acetyltransferase GCN5
2674842 2703653 28811 LOCUS_22950 prolyl 4-hydroxylase subunit alpha
2674842 2703653 28811 LOCUS_22970 GCN5 family N-acetyltransferase
2674842 2703653 28811 LOCUS_22980 N-acetyltransferase GCN5
2674842 2703653 28811 LOCUS_23010 ABC transporter substrate-binding protein
2674842 2703653 28811 LOCUS_23040 membrane protein
2674842 2703653 28811 LOCUS_23060 phage integrase
2674842 2703653 28811 LOCUS_23110 integrase
2674842 2703653 28811 LOCUS_23120 transposase
2674842 2703653 28811 LOCUS_23180 molecular chaperone DnaJ
2987651 3023065 35414 tnpA LOCUS_25460 IS91 family transposase
2987651 3023065 35414 LOCUS_25470 integrase
2987651 3023065 35414 LOCUS_25500 esterase
2987651 3023065 35414 tnpA LOCUS_25520 ISAs1 family transposase
2987651 3023065 35414 LOCUS_25570 restriction endonuclease subunit M
2987651 3023065 35414 LOCUS_25580 peptide ABC transporter substrate-binding protein
2987651 3023065 35414 LOCUS_25590 restriction modification system DNA specificity domain-containing protein
2987651 3023065 35414 LOCUS_25600 DNA-binding protein
2987651 3023065 35414 LOCUS_25610 "type I restriction-modification system
2987651 3023065 35414 LOCUS_25710 replication protein
2987651 3023065 35414 LOCUS_25820 replication protein
3008370 3023264 14894 LOCUS_25710 replication protein
3008370 3023264 14894 LOCUS_25820 replication protein
3040353 3063054 22701 ald LOCUS_26030 alanine dehydrogenase
3040353 3063054 22701 trxB LOCUS_26040 thioredoxin reductase
3040353 3063054 22701 rplT LOCUS_26050 50S ribosomal protein L20
3040353 3063054 22701 rpmI LOCUS_26060 50S ribosomal protein L35
3040353 3063054 22701 infC LOCUS_26070 translation initiation factor IF-3
3040353 3063054 22701 thrS LOCUS_26080 threonine--tRNA ligase
3040353 3063054 22701 LOCUS_26100 CPXCG motif-containing cysteine-rich protein
3040353 3063054 22701 ribC LOCUS_26110 riboflavin synthase subunit alpha
3040353 3063054 22701 norM LOCUS_26120 putative multidrug resistance protein NorM
3040353 3063054 22701 fdhD LOCUS_26130 sulfurtransferase FdhD
3040353 3063054 22701 fdhE LOCUS_26140 protein FdhE
3040353 3063054 22701 fdnI LOCUS_26150 formate dehydrogenase subunit gamma
3040353 3063054 22701 fdnG LOCUS_26170 formate dehydrogenase-N subunit alpha
3512513 3525569 13056 LOCUS_29950 nucleoid-associated protein
3512513 3525569 13056 dnaX LOCUS_29960 DNA polymerase III subunit gamma/tau
3512513 3525569 13056 apt LOCUS_29970 adenine phosphoribosyltransferase
3512513 3525569 13056 LOCUS_29980 inner membrane protein
3512513 3525569 13056 LOCUS_29990 DUF2063 domain-containing protein
3512513 3525569 13056 LOCUS_30000 UPF0276 protein
3512513 3525569 13056 dusC LOCUS_30020 tRNA-dihydrouridine(16) synthase
3512513 3525569 13056 LOCUS_30030 conjugal transfer protein TraR
3512513 3525569 13056 LOCUS_30040 TonB-dependent receptor
3512513 3525569 13056 tnpA LOCUS_30050 ISAs1 family transposase
4080518 4113038 32520 LOCUS_34520 UPF0125 protein
4080518 4113038 32520 yfjG LOCUS_34530 ubiquinone-binding protein
4080518 4113038 32520 smpB LOCUS_34540 SsrA-binding protein
4080518 4113038 32520 intA LOCUS_34550 integrase
4080518 4113038 32520 LOCUS_34560 ADP-ribose-binding domain-containing protein
4080518 4113038 32520 LOCUS_34580 metal-dependent hydrolase
4080518 4113038 32520 LOCUS_34590 type I restriction enzyme
4080518 4113038 32520 LOCUS_34610 restriction endonuclease subunit S
4080518 4113038 32520 mrr LOCUS_34620 restriction endonuclease
4080518 4113038 32520 LOCUS_34630 DNA-binding protein
4080518 4113038 32520 LOCUS_34640 DNA repair protein RadC
4080518 4113038 32520 yfjZ LOCUS_34660 Mu phage lytic protein YfjZ
4080518 4113038 32520 LOCUS_34680 site-specific integrase
4319152 4408145 88993 LOCUS_36460 iso-IS10R ORF
4319152 4408145 88993 LOCUS_36530 DNA repair protein RadC
4319152 4408145 88993 LOCUS_36580 cobalamin synthase
4319152 4408145 88993 LOCUS_36650 BCCT family transporter
4319152 4408145 88993 LOCUS_36660 3'-5' exonuclease
4319152 4408145 88993 LOCUS_36670 cyclic nucleotide-binding protein
4319152 4408145 88993 LOCUS_36690 GGDEF domain-containing protein
4319152 4408145 88993 LOCUS_36740 IS110 family transposase
4319152 4408145 88993 trhC LOCUS_36790 plasmid transfer protein
4319152 4408145 88993 LOCUS_36820 N-acetyltransferase GCN5
4319152 4408145 88993 LOCUS_36930 "conjugative coupling factor TraD
4319152 4408145 88993 LOCUS_36950 Mrr restriction system protein
4319152 4408145 88993 LOCUS_36960 DEAD/DEAH box helicase
4319152 4408145 88993 LOCUS_36970 site-specific DNA-methyltransferase
4319152 4408145 88993 LOCUS_36990 helicase
4319152 4408145 88993 LOCUS_37000 WYL domain-containing protein
4319152 4408145 88993 LOCUS_37020 DNA polymerase III subunit epsilon
4319152 4408145 88993 umuD LOCUS_37040 protein impA'
4319152 4408145 88993 umuC LOCUS_37050 DNA polymerase V subunit UmuC
4319152 4408145 88993 LOCUS_37060 ATPase
4319152 4408145 88993 LOCUS_37110 integrase
4319152 4408145 88993 nlpI LOCUS_37130 lipoprotein NlpI
4319152 4408145 88993 pnp LOCUS_37140 polyribonucleotide nucleotidyltransferase
4319152 4408145 88993 LOCUS_37150 GGDEF-domain containing protein
4319152 4408145 88993 rpsO LOCUS_37160 30S ribosomal protein S15
4319152 4408145 88993 truB LOCUS_37170 tRNA pseudouridine synthase B
4319152 4408145 88993 rbfA LOCUS_37180 ribosome-binding factor A
4319152 4408145 88993 infB LOCUS_37190 translation initiation factor IF-2
4319152 4408145 88993 nusA LOCUS_37200 transcription termination/antitermination protein NusA
4319152 4408145 88993 rimP LOCUS_37210 ribosome maturation factor RimP
4319152 4408145 88993 secG LOCUS_37220 preprotein translocase subunit SecG
4319152 4408145 88993 tpiA LOCUS_37230 triosephosphate isomerase
4319152 4408145 88993 glmM LOCUS_37240 phosphoglucosamine mutase

Genomic Island in Shewanella.sp SdM1

The Shewanella. sp SdM1 was described as enviroment enviroment strain and it genome present 14 Genomic Island asociated to diverse function

Island_start Island_end Length Gene_ID Locus Product
1548681 1560640 11959 LOCUS_33550 resolvase
1548681 1560640 11959 LOCUS_33570 ImmA/IrrE family metallo-endopeptidase
1548681 1560640 11959 rsmI LOCUS_33610 ribosomal RNA small subunit methyltransferase I
1548681 1560640 11959 lppC LOCUS_33630 penicillin-binding protein activator
1728407 1738630 10223 LOCUS_37560 transcriptional regulator
1728407 1738630 10223 LOCUS_37550 transcriptional regulator
1728407 1738630 10223 LOCUS_37540 type III secretion protein
1728407 1738630 10223 LOCUS_37500 outer membrane protein
1728407 1738630 10223 LOCUS_37490 type III secretion protein
1905743 1916241 10498 LOCUS_39160 DDE transposase
1905743 1916241 10498 LOCUS_39170 TonB-dependent receptor
1905743 1916241 10498 glmU LOCUS_39180 bifunctional protein GlmU
1905743 1916241 10498 atpC LOCUS_39190 ATP synthase epsilon chain
1905743 1916241 10498 atpD LOCUS_39200 ATP synthase subunit beta
1905743 1916241 10498 atpG LOCUS_39210 ATP synthase gamma chain
1905743 1916241 10498 atpA LOCUS_39220 ATP synthase subunit alpha
1905743 1916241 10498 atpH LOCUS_39230 ATP synthase subunit delta
1905743 1916241 10498 atpF LOCUS_39240 ATP synthase subunit b
1905743 1916241 10498 atpE LOCUS_39250 ATP synthase subunit c
1984803 2056714 71911 LOCUS_29080 transposase
1984803 2056714 71911 LOCUS_29090 transposase
1984803 2056714 71911 LOCUS_29100 transposase
1984803 2056714 71911 LOCUS_29140 DUF2384 domain-containing protein
1984803 2056714 71911 LOCUS_29190 phage integrase
1984803 2056714 71911 LOCUS_29200 diguanylate cyclase response regulator
1984803 2056714 71911 LOCUS_29250 4'-phosphopantetheinyl transferase
1984803 2056714 71911 LOCUS_29260 thioesterase
1984803 2056714 71911 LOCUS_29280 asparagine synthetase B
1984803 2056714 71911 LOCUS_29300 MFS transporter
1984803 2056714 71911 LOCUS_29340 hydroxyneurosporene-O-methyltransferase
1984803 2056714 71911 hisC LOCUS_29360 histidinol-phosphate aminotransferase
1984803 2056714 71911 LOCUS_29430 thioesterase
1984803 1997807 13004 LOCUS_29080 transposase
1984803 1997807 13004 LOCUS_29090 transposase
1984803 1997807 13004 LOCUS_29100 transposase
1984803 1997807 13004 LOCUS_29140 DUF2384 domain-containing protein
2576822 2587803 10981 LOCUS_22480 diguanylate phosphodiesterase
2576822 2587803 10981 LOCUS_22490 SAM-dependent methyltransferase
2576822 2587803 10981 LOCUS_22500 membrane protein
2576822 2587803 10981 LOCUS_22520 maturase
2576822 2587803 10981 LOCUS_22530 DNA-binding protein
2576822 2587803 10981 purC LOCUS_22540 phosphoribosylaminoimidazole-succinocarboxamide synthase
2576822 2587803 10981 LOCUS_22550 activator of HSP90 ATPase
2740543 2764811 24268 LOCUS_23930 Cro/Cl family transcriptional regulator
2740543 2764811 24268 LOCUS_24090 capsid portal protein
2740543 2764811 24268 LOCUS_24100 oxidoreductase
2740543 2764811 24268 O LOCUS_24110 phage capsid scaffolding protein
2740543 2764811 24268 LOCUS_24120 phage capsid protein
2740543 2764811 24268 LOCUS_24130 bacteriophage terminase endonuclease subunit
2740543 2764811 24268 LOCUS_24140 capsid completion protein
2740543 2764811 24268 LOCUS_24150 tail protein X
2740543 2764811 24268 LOCUS_24180 peptidoglycan-binding protein
2740543 2764811 24268 R LOCUS_24210 tail protein
2740543 2764811 24268 LOCUS_24220 bacteriophage tail completion protein S
2805973 2850327 44354 LOCUS_41610 DNA repair protein RadC
2805973 2850327 44354 LOCUS_41590 ATPase
2805973 2850327 44354 LOCUS_41580 integrase
2805973 2850327 44354 rulA LOCUS_41520 DNA polymerase V
2805973 2850327 44354 rulB LOCUS_41510 DNA polymerase V subunit UmuC
2805973 2850327 44354 LOCUS_41460 DNA-binding protein
2805973 2850327 44354 LOCUS_41410 LysR family transcriptional regulator
2805973 2850327 44354 assT LOCUS_41390 aryl-sulfate sulfotransferase
2805973 2850327 44354 LOCUS_41380 thiol:disulfide interchange protein
2805973 2850327 44354 dsbI LOCUS_41370 putative protein-disulfide oxidoreductase DsbI
2805973 2850327 44354 LOCUS_41360 lysine transporter LysE
2805973 2850327 44354 trpI LOCUS_41350 LysR family transcriptional regulator
2805973 2850327 44354 LOCUS_41340 TonB-dependent receptor
2805973 2850327 44354 LOCUS_41310 peptidase
2805973 2850327 44354 LOCUS_41300 Cd(II)/Pb(II)-responsive transcriptional regulator
2805973 2850327 44354 irgA LOCUS_41290 ligand-gated channel protein
3615336 3632391 17055 wzz LOCUS_00820 LPS biosynthesis protein
3615336 3632391 17055 wbpA LOCUS_00810 UDP-N-acetyl-d-glucosamine 6-dehydrogenase WbpA
3615336 3632391 17055 wbpP LOCUS_00800 UDP-GlkcNAc C4 epimerase WbpP
3615336 3632391 17055 rfbB LOCUS_00790 "dTDP-glucose 4
3615336 3632391 17055 rmlA LOCUS_00780 glucose-1-phosphate thymidylyltransferase
3615336 3632391 17055 LOCUS_00770 polysaccharide biosynthesis protein
3615336 3632391 17055 vioB LOCUS_00760 transferase
3615336 3632391 17055 wzx LOCUS_00750 polysaccharide biosynthesis protein
3615336 3632391 17055 wbnI LOCUS_00740 glycosyl transferase
3615336 3632391 17055 wzy LOCUS_00720 O-antigen polymerase Wzy
3615336 3632391 17055 LOCUS_00710 glycosyl transferase
3615336 3632391 17055 wbpQ LOCUS_00700 asparagine synthetase B
3615336 3632391 17055 LOCUS_00690 glycosyl transferase family 1
3615336 3632391 17055 LOCUS_00680 UDP-glucose 4-epimerase
4436027 4498057 62030 LOCUS_10550 metallophosphatase
4436027 4498057 62030 LOCUS_10690 baseplate protein
4436027 4498057 62030 LOCUS_10700 type VI secretion protein
4436027 4498057 62030 LOCUS_10720 peptidoglycan-binding protein
4436027 4498057 62030 LOCUS_10870 transposase
4436027 4498057 62030 hmrR LOCUS_10900 HTH-type transcriptional regulator HmrR
4436027 4498057 62030 actP LOCUS_10920 copper-translocating P-type ATPase
4436027 4498057 62030 LOCUS_10940 resistance-nodulation-cell division efflux transporter
4436027 4498057 62030 LOCUS_10950 resistance-nodulation-cell division efflux membrane fusion protein
4484288 4498057 13769 hmrR LOCUS_10900 HTH-type transcriptional regulator HmrR
4484288 4498057 13769 actP LOCUS_10920 copper-translocating P-type ATPase
4484288 4498057 13769 LOCUS_10940 resistance-nodulation-cell division efflux transporter
4484288 4498057 13769 LOCUS_10950 resistance-nodulation-cell division efflux membrane fusion protein
4670101 4683766 13665 LOCUS_38380 UPF0227 protein
4769972 4786651 16679 LOCUS_42590 transposase for insertion sequence element IS1111A
4769972 4786651 16679 hisG LOCUS_42600 ATP phosphoribosyltransferase
4769972 4786651 16679 hisD LOCUS_42610 histidinol dehydrogenase
4769972 4786651 16679 hisC LOCUS_42620 histidinol-phosphate aminotransferase
4769972 4786651 16679 hisB LOCUS_42630 histidine biosynthesis bifunctional protein HisB
4769972 4786651 16679 hisA LOCUS_42640 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)me thylideneamino] imidazole-4-carboxamide isomerase
4769972 4786651 16679 hisF LOCUS_42650 imidazole glycerol phosphate synthase subunit HisF
4769972 4786651 16679 hisI LOCUS_42660 histidine biosynthesis bifunctional protein HisIE
4769972 4786651 16679 tyrP LOCUS_42670 tyrosine transporter TyrP
4769972 4786651 16679 LOCUS_42680 C4-dicarboxylate ABC transporter
4769972 4786651 16679 LOCUS_42690 YnbE family lipoprotein
4922100 4960894 38794 LOCUS_25700 flavocytochrome c
4922100 4960894 38794 LOCUS_25710 cytochrome c
4922100 4960894 38794 LOCUS_25720 outer membrane beta barrel protein
4922100 4960894 38794 LOCUS_25740 periplasmic RmlC-type Cupin domain family protein
4922100 4960894 38794 LOCUS_25770 membrane protein
4922100 4960894 38794 LOCUS_25780 redox-active disulfide protein
4922100 4960894 38794 ktrA LOCUS_25790 potassium transporter TrkA
4922100 4960894 38794 ktrB LOCUS_25800 Ktr system potassium transporter B
4922100 4960894 38794 LOCUS_25810 FAD:protein FMN transferase
4922100 4960894 38794 LOCUS_25820 Na+/H+ antiporter NhaD
4922100 4960894 38794 uppP2 LOCUS_25830 undecaprenyl-diphosphatase 2
4922100 4960894 38794 motB LOCUS_25840 flagellar motor protein MotB
4922100 4960894 38794 motA LOCUS_25850 chemotaxis protein MotA
4922100 4960894 38794 LOCUS_25860 methyl-accepting chemotaxis protein
4922100 4960894 38794 LOCUS_25890 recombinase
4922100 4960894 38794 LOCUS_25920 DNA-binding protein
4922100 4960894 38794 prtR LOCUS_25970 HTH-type transcriptional regulator PrtR
4922100 4960894 38794 LOCUS_26000 FRG domain-containing protein
5066027 5079171 13144 LOCUS_42350 cytosine-specific methyltransferase
5066027 5079171 13144 LOCUS_42360 type II restriction-modification system endonuclease
5066027 5079171 13144 LOCUS_42380 prevent-host-death protein

Probiotic and pathogenic strains comparison

This analysis were focused on pathogenic and probiotic strains comparison by Tarsynflow, which identified the specific genes on pathogenic and their absent on probiotic strain.

Entry protein names organism
A0A073KRP2 L-lactate permease Shewanella xiamenensis
A0A380B106 L-seryl-tRNA(Sec) selenium transferase (EC 2.9.1.1) (Selenocysteine synthase) (Sec synthase) (Selenocysteinyl-tRNA(Sec) synthase) Shewanella morhuae
A0A9Q8S687 histidine kinase (EC 2.7.13.3) Shewanella sp. JNE2
A0A161WSP6 Endoribonuclease L-PSP/chorismate mutase-like domain-containing protein Shewanella baltica
A0A161WUQ9 LuxR family transcriptional regulator Shewanella baltica
A0A1E3UTG5 DUF4274 domain-containing protein Shewanella xiamenensis
A0A220US46 Two-component system response regulator Shewanella bicestrii
A0A2M7HTT6 Sodium:alanine symporter Shewanella sp. CG12_big_fil_rev_8_21_14_0_65_47_15
A0A4R2FJ85 Two-component system response regulator AdeR Shewanella fodinae
A0A501XHX2 CDP-glycerol--glycerophosphate glycerophosphotransferase Shewanella sp. LC6
A0A5B8QSE5 TetR/AcrR family transcriptional regulator Shewanella decolorationis
A0A9X2WTL9 histidine kinase (EC 2.7.13.3) Shewanella septentrionalis
A3D7Z8 Sodium/calcium exchanger membrane region Shewanella baltica (strain OS155 / ATCC BAA-1091)